| title: " Nanostring_validation_report“ |
| author: “Sridhar” |
| date: “8/22/2017” |
| output: html |
See email:
#NOTE CHANGE IN SAMPLE IDS BASED ON CARA’S EMAIL On Aug 9, 2017, at 5:37 PM, Shirai, Cara clunn@wustl.edu wrote:
Sid,
Yes, this is what I discussed with you Monday. The mouse # is correct and will dictate treatment.
The sude vs veh is switched.
Thanks, Cara
altough we changed the sample names as per the sample submission forms, mouse id allocated to veh in each cell type actually belonged to 5 hours sudemycin treated samples so we need change the read names after first name change based on file names.
Mouse ids 1,2,6 belong vehicle and mouse ids 8,9,11 belong to sudemycin treated cells at 5 hours
Column trasnfomation from file names to sample id ***
Load data for each cell type and change legend based on correct sample names
bul.both = read.csv("normalize_bulk_both.csv", sep = ',', header = T, stringsAsFactors = F)
bul.both = plyr::rename(bul.both, c(
"X5hr.11.BULK.VEH.11" = "X5hr.11.BULK.SUDE.11",
"X5hr.8.BULK.VEH.8" = "X5hr.8.BULK.SUDE.8",
"X5hr.9.BULK.VEH.9" = "X5hr.9.BULK.SUDE.9",
"X5hr.2.BULK.SUDE.2" = "X5hr.2.BULK.VEH.2",
"X5hr.6.BULK.SUDE.6" = "X5hr.6.BULK.VEH.6",
"X5hr.1.BULK.SUDE.1" = "X5hr.1.BULK.VEH.1"))
dim(bul.both)
[1] 122 13
cellb.both = read.csv("normalize_bcell_both.csv", sep = ',', header = T, stringsAsFactors = F)
cellb.both = plyr::rename(cellb.both, c(
"X5hr.8.B_CELL.VEH.8" = "X5hr.8.B_CELL.SUDE.8",
"X5hr.9.B_CELL.VEH.9" = "X5hr.9.B_CELL.SUDE.9",
"X5hr.11.B_CELL.VEH.11" = "X5hr.11.B_CELL.SUDE.11",
"X5hr.6.B_CELL.SUDE.6" = "X5hr.6.B_CELL.VEH.6",
"X5hr.1.B_CELL.SUDE.1" = "X5hr.1.B_CELL.VEH.1",
"X5hr.2.B_CELL.SUDE.2" = "X5hr.2.B_CELL.VEH.2"))
dim(cellb.both)
[1] 122 13
myec.both = read.csv("normalize_myeloid_both.csv", sep = ',', header = T, stringsAsFactors = F)
myec.both = plyr::rename(myec.both, c(
"X5hr.8.MYE.VEH.8" = "X5hr.8.MYE.SUDE.8",
"X5hr.9.MYE.VEH.9" = "X5hr.9.MYE.SUDE.9",
"X5hr.11.MYE.VEH.11" = "X5hr.11.MYE.SUDE.11",
"X5hr.2.MYE.SUDE.2" = "X5hr.2.MYE.VEH.2",
"X5hr.1.MYE.SUDE.1" = "X5hr.1.MYE.VEH.1",
"X5hr.6.MYE.SUDE.6" = "X5hr.6.MYE.VEH.6"))
dim(myec.both)
[1] 122 13
valid.probes = read.table("validated_probes.txt", sep='\t', stringsAsFactors = F)
dim(valid.probes)
[1] 73 1
####Number of valid probes bulk cells bulk cells have 73, 13 probes in common
dim(bul.valid.5all.z)
## [1] 49 7
dim(bul.valid.2all.z)
## [1] 49 7
dim(bul.valid.24all.z)
## [1] 48 7
[1] 73 13 [1] 53 13
dim(cellb.valid.5all.z)
## [1] 39 7
dim(cellb.valid.2all.z)
## [1] 48 7
dim(cellb.valid.24all.z)
## [1] 37 7
[1] 73 13
dim(myec.valid.5all.z)
## [1] 39 7
dim(myec.valid.2all.z)
## [1] 43 7
dim(myec.valid.24all.z)
## [1] 37 7